WebClass DuplicationMetrics. java.lang.Object. htsjdk.samtools.metrics.MetricBase. picard.sam.DuplicationMetrics. public class DuplicationMetrics extends … http://www.htslib.org/algorithms/duplicate.html

Filtering with SAMTools - Core NGS Tools - UT Austin Wikis

WebDuplicate Marking Duplicates are defined as having multiple templates whose aligned 5’ coordinates match. For a paired-end template this requires both primary reads to have … WebApr 8, 2024 · The dedup option of bamUtil determines duplicates in a coordinate sorted SAM/BAM file. It either marks or removes the lower quality duplicates. This tool also contains the option to perform recalibration. NOTE: This tool does not properly work on templates that have more than 2 segments. linux change owner of symlink

alignment - Difference between samtools mark duplicates and samtool…

Websamtools fixmate -m namesort.bam fixmate.bam # Markdup needs position order samtools sort -o positionsort.bam fixmate.bam # Finally mark duplicates. Use -r flag to remove … WebAlso, multiBamSummary in deepTools can be used to check the correlations between BAM files before merging. Shifting reads. In the first ATAC-seq paper (Buenrostro et al., 2013), all reads aligning to the + strand were … WebDUPLICATE PAIR: reads in a duplicate pair. DUPLICATE SINGLE: single read duplicates. DUPLICATE PAIR OPTICAL: optical duplicate paired reads. DUPLICATE SINGLE OPTICAL: … house for bloxburg 2 story little home